QQ plot
That refers to "normally" distributed data (see Greg Snow's comment below the one you cite). P-values are not necessarily normally distributed as you can see, and they must have a non-zero mean. Jim
On Wed, Nov 13, 2019 at 7:07 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:
Hi, what I know so far that this kind of QQ plot is an indication that data has non zero mean: https://stats.stackexchange.com/questions/280634/how-to-interpret-qq-plot-not-on-the-line but is that an indication that something is wrong with the analysis? Thanks Ana On Tue, Nov 12, 2019 at 2:00 PM Jim Lemon <drjimlemon at gmail.com> wrote:
I thought about this and did a little study of GWAS and the use of p-values to assess significant associations. As Ana's plot begins at values of about 0.001, this seems to imply that almost everything in the genome is associated to some degree. One expects that most SNPs will not be associated with a particular condition (p~1), so perhaps something is going wrong in the calculations that produce the p-values. Jim On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) <malone at malonequantitative.com> wrote:
I agree with Abby. That would defeat the purpose of a QQ plot. On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdle.a at gmail.com> wrote:
Hi I'm not familiar with the qqman package, or GWAS studies. However, my guess would be that you're *not* supposed to change the position of the line. On Tue, Nov 12, 2019 at 11:48 AM Ana Marija <sokovic.anamarija at gmail.com> wrote:
Hi, I was using this library, qqman https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html to create QQ plot, attached. How would I change this default abline to start from the beginning of my QQ line? This is my code: qq(dd$P, main = "Q-Q plot of GWAS p-values") Thanks Ana
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